Special Issue "DNA Barcoding and Metabarcoding of Complex Matrices"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (10 February 2019)

Special Issue Editors

Guest Editor
Prof. Massimo Labra

Department of Biotechnology and Biosciences, Universita degli Studi di Milano - Bicocca, Milan, Italy
Website | E-Mail
Phone: 0039 0264483472
Interests: plant biology, plant evolution, biodiversity, agrobiodiversity, botanicals, food matrices, food traceability, DNA barcoding
Guest Editor
Dr. Andrea Galimberti

Dept. Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
Website | E-Mail
Phone: 0039 0264483412
Interests: integrated taxonomy, DNA barcoding, metazoans, biological interactions, food authenticity, High Throughput Sequencing
Guest Editor
Assoc. Prof. Hugo De Boer

Plant Evolution and DNA Metabarcoding Group, Natural History Museum, University of Oslo, Oslo, Norway
Website | E-Mail
Phone: +47 98126030
Interests: Molecular identification of Plants; Plant DNA Metabarcoding; Plant Phylogenomics; Herbal Authenticity; Food and Drug Safety; Illegal Plant Trade

Special Issue Information

Dear Colleagues,

DNA barcoding is a molecular and bioinformatics tool that aims at identifying organisms’ species. The rationale of this approach is quite simple: Through the analysis of the variability in a single or in a few standard molecular marker(s), it is possible to discriminate biological entities. In the last fifteen years, this approach has largely been used to address taxonomic issues, as well as to achieve a reliable traceability system for raw materials, processed food items and other commercial products. Recently, due to the continuous advances in the field of high throughput sequencing, more and more applications have become possible in the field of molecular identification, especially with the development of DNA metabarcoding. This powerful approach enables simultaneous detection of multiple species in complex biological matrices. DNA metabarcoding can be adopted with high reliability and sensitivity, from environmental samples (e.g., soil, water and feces) to food products. Moreover, this revolutionizing identification strategy is also useful to analyze highly-processed materials containing degraded DNA, such as plant extracts, manufactured food, cosmetics or drugs plant-based products. Both DNA barcoding and metabarcoding demand suitable bioinformatics tools to achieve an efficient data processing and well-populated and verified public (or private) databases for the identification.

This Special Issue is devoted to the advances in DNA barcoding and metabarcoding to analyze complex matrices with the main goals of i) elucidating the technical and bioinformatical advances currently available for these tools; ii) defining the possible fields of application; and iii) the effectiveness of these approaches in the research and technology transfer strategy. The editors also invite submissions on advanced approaches, including DNA metagenomics, target-enrichment sequencing, and marker mining from genome skimming data.

We cordially invite researchers working actively in these fields to submit their original research manuscripts to this Special Issue.

Prof. Massimo Labra
Dr. Andrea Galimberti
Assoc. Prof. Hugo de Boer
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Botanicals
  • Diet and Microbiome characterization
  • DNA taxonomy
  • Environmental matrices
  • Fast identification approaches
  • Food Authentication and traceability
  • Food matrices
  • High Throughput Sequencing
  • Molecular markers

Published Papers (4 papers)

View options order results:
result details:
Displaying articles 1-4
Export citation of selected articles as:

Research

Open AccessArticle Improved Protocols of ITS1-Based Metabarcoding and Their Application in the Analysis of Plant-Containing Products
Received: 16 December 2018 / Revised: 28 January 2019 / Accepted: 4 February 2019 / Published: 7 February 2019
PDF Full-text (1042 KB) | Supplementary Files
Abstract
Plants are widely used for food and beverage preparation, most often in the form of complex mixtures of dried and ground parts, such as teas, spices or herbal medicines. Quality control of such products is important due to the potential health risks from [...] Read more.
Plants are widely used for food and beverage preparation, most often in the form of complex mixtures of dried and ground parts, such as teas, spices or herbal medicines. Quality control of such products is important due to the potential health risks from the presence of unlabelled components or absence of claimed ones. A promising approach to analyse such products is DNA metabarcoding due to its high resolution and sensitivity. However, this method’s application in food analysis requires several methodology optimizations in DNA extraction, amplification and library preparation. In this study, we present such optimizations. The most important methodological outcomes are the following: 1) the DNA extraction method greatly influences amplification success; 2) the main problem for the application of metabarcoding is DNA purity, not integrity or quantity; and 3) the “non-amplifiable” samples can be amplified with polymerases resistant to inhibitors. Using this optimized workflow, we analysed a broad set of plant products (teas, spices and herbal remedies) using two NGS platforms. The analysis revealed the problem of both the presence of extraneous components and the absence of labelled ones. Notably, for teas, no correlation was found between the price and either the absence of labelled components or presence of unlabelled ones; for spices, a negative correlation was found between the price and presence of unlabelled components. Full article
(This article belongs to the Special Issue DNA Barcoding and Metabarcoding of Complex Matrices)
Open AccessArticle A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae)
Genes 2018, 9(12), 637; https://doi.org/10.3390/genes9120637
Received: 27 October 2018 / Revised: 5 December 2018 / Accepted: 10 December 2018 / Published: 17 December 2018
PDF Full-text (534 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we [...] Read more.
Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii. Full article
(This article belongs to the Special Issue DNA Barcoding and Metabarcoding of Complex Matrices)
Figures

Figure 1

Open AccessArticle Trade in Zambian Edible Orchids—DNA Barcoding Reveals the Use of Unexpected Orchid Taxa for Chikanda
Genes 2018, 9(12), 595; https://doi.org/10.3390/genes9120595
Received: 24 October 2018 / Revised: 17 November 2018 / Accepted: 22 November 2018 / Published: 30 November 2018
PDF Full-text (1189 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In Zambia, wild edible terrestrial orchids are used to produce a local delicacy called chikanda, which has become increasingly popular throughout the country. Commercialization puts orchid populations in Zambia and neighbouring countries at risk of overharvesting. Hitherto, no study has documented which [...] Read more.
In Zambia, wild edible terrestrial orchids are used to produce a local delicacy called chikanda, which has become increasingly popular throughout the country. Commercialization puts orchid populations in Zambia and neighbouring countries at risk of overharvesting. Hitherto, no study has documented which orchid species are traded on local markets, as orchid tubers are difficult to identify morphologically. In this study, the core land-plant DNA barcoding markers rbcL and matK were used in combination with nrITS to determine which species were sold in Zambian markets. Eighty-two interviews were conducted to determine harvesting areas, as well as possible sustainability concerns. By using nrITS DNA barcoding, a total of 16 orchid species in six different genera could be identified. Both rbcL and matK proved suitable to identify the tubers up to the genus or family level. Disa robusta, Platycoryne crocea and Satyrium buchananii were identified most frequently and three previously undocumented species were encountered on the market. Few orchid species are currently listed on the global International Union for the Conservation of Nature (IUCN) Red List. Local orchid populations and endemic species could be at risk of overharvesting due to the intensive and indiscriminate harvesting of chikanda orchids, and we therefore encourage increased conservation assessment of terrestrial African orchids. Full article
(This article belongs to the Special Issue DNA Barcoding and Metabarcoding of Complex Matrices)
Figures

Graphical abstract

Open AccessArticle Authenticity Testing and Detection of Eurycoma longifolia in Commercial Herbal Products Using Bar-High Resolution Melting Analysis
Received: 3 June 2018 / Revised: 30 July 2018 / Accepted: 7 August 2018 / Published: 12 August 2018
PDF Full-text (1072 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The present study demonstrated High Resolution Melting (HRM) analysis combined with DNA barcode (Bar-HRM) as a fast and highly sensitive technique for detecting adulterants in Eurycoma longifolia commercial herbal products. Targeting the DNA barcoding of the chloroplastic region-ribulose biphosphate carboxylase large chain (rbcL) [...] Read more.
The present study demonstrated High Resolution Melting (HRM) analysis combined with DNA barcode (Bar-HRM) as a fast and highly sensitive technique for detecting adulterants in Eurycoma longifolia commercial herbal products. Targeting the DNA barcoding of the chloroplastic region-ribulose biphosphate carboxylase large chain (rbcL) and the nuclear ribosomal region- internal transcribed spacer 2 (ITS2), PCR amplification and HRM analysis using saturated Eva green dye as the source of fluorescence signals, was accomplished by employing a real-time cycler. The results were further validated by sequencing to identify unknown sequence from Genbank database and to generate phylogenetic tree using neighbour joint (NJ) analysis. Both of the DNA markers exhibited a distinguishable melting temperature and shape of the normalised curve between the reference and the adulterants. In the case of species identification, ITS2 was more successful in differentiating between species. Additionally, detection of admixture sample containing small traces of targeted E. longifolia DNA (w/v) can be detected as low as 5% for rbcL and less than 1% for ITS2, proving the sensitivity and versatility of the HRM analysis. In conclusion, the Bar-HRM analysis is a fast and reliable technique that can effectively detect adulterants in herbal products. Therefore, this will be beneficial for regulatory agencies in order to regulate food safety issues. Full article
(This article belongs to the Special Issue DNA Barcoding and Metabarcoding of Complex Matrices)
Figures

Figure 1

Genes EISSN 2073-4425 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top